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linux - Safest way to write into /etc from php application?

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Solution:

If the Apache user (www-data) can write or modify/etc all the system is compromised.

If any user of the PHP application can change the demon's configuration the behaviour may be a mess. You told about "users", changing simultaneously that config file.

As @quentin says use a database if you need persistence; or an application file (not in/etc or other system directory).

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